Select only primary alignments and you should get one per read.
On 3 July 2014 09:36, Zhao, Shanrong <shanrong.z...@pfizer.com> wrote:
> For unmapped reads, I believe
>
> samtools view *-f* 4 file.bam > unmapped.bam
>
>
>
> However, for mapped reads, the command line maybe not work properly unless
> “no multiple mapping read in BAM”.
>
> samtools view -F 4 file.bam > mapped.sam
>
>
>
> I assume samtools does not check whether a read is mapped to multiple
> locations. For pair-ended sequencing, the mapping is more complex. In
> addition to unmapped reads, a read pair can be uniquely mapped or multiple
> location. Likewise, for singleton, one read can be mapped to multiple
> locations or uniquely with its mate unapped.
>
>
>
> What I want is: extract mapped reads and write them into FASTQ files. For
> multiple mapping reads, only write them once. Any advice?
>
>
>
> Thank you,
>
> Shanrong
>
>
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